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Sangree AK, Angireddy R, Bryant LM, Layo-Carris DE, Lubin EE, Wang XM, Clark KJ, Durham EE, Bhoj EJ. A novel iPSC model of Bryant-Li-Bhoj neurodevelopmental syndrome demonstrates the role of histone H3.3 in neuronal differentiation and maturation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.26.609745. [PMID: 39253491 PMCID: PMC11382994 DOI: 10.1101/2024.08.26.609745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Background Bryant-Li-Bhoj neurodevelopmental syndrome (BLBS) is neurogenetic disorder caused by variants in H3-3A and H3-3B, the two genes that encode the histone H3.3 protein. Ninety-nine percent of individuals with BLBS show developmental delay/intellectual disability, but the mechanism by which variants in H3.3 result in these phenotypes is not yet understood. As a result, only palliative interventions are available to individuals living with BLBS. Methods Here, we investigate how one BLBS-causative variant, H3-3B p.Leu48Arg (L48R), affects neurodevelopment using an induced pluripotent stem cell (iPSC) model differentiated to 2D neural progenitor cells (NPCs), 2D forebrain neurons (FBNs), and 3D dorsal forebrain organoids (DFBOs). We employ a multi-omic approach in the 2D models to quantify the resulting changes in gene expression and chromatin accessibility. We used immunofluorescence (IF) staining to define the identities of cells in the 3D DFBOs. Results In the 2D systems, we found dysregulation of both gene expression and chromatin accessibility of genes important for neuronal fate, maturation, and function in H3.3 L48R compared to control. Our work in 3D organoids corroborates these findings, demonstrating altered proportions of radial glia and mature neuronal cells. Conclusions These data provide the first mechanistic insights into the pathogenesis of BLBS from a human-derived model of neurodevelopment, which suggest that the L48R increases H3-3B expression, resulting in the hyper-deposition of H3.3 into the nucleosome which underlies changes in gene expression and chromatin accessibility. Functionally, this causes dysregulation of cell adhesion, neurotransmission, and the balance between excitatory and inhibitory signaling. These results are a crucial step towards preclinical development and testing of targeted therapies for this and related disorders.
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Kobren SN, Moldovan MA, Reimers R, Traviglia D, Li X, Barnum D, Veit A, Corona RI, Carvalho Neto GDV, Willett J, Berselli M, Ronchetti W, Nelson SF, Martinez-Agosto JA, Sherwood R, Krier J, Kohane IS, Sunyaev SR. Joint, multifaceted genomic analysis enables diagnosis of diverse, ultra-rare monogenic presentations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580158. [PMID: 38405764 PMCID: PMC10888768 DOI: 10.1101/2024.02.13.580158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Genomics for rare disease diagnosis has advanced at a rapid pace due to our ability to perform "N-of-1" analyses on individual patients with ultra-rare diseases. The increasing sizes of ultra-rare disease cohorts internationally newly enables cohort-wide analyses for new discoveries, but well-calibrated statistical genetics approaches for jointly analyzing these patients are still under development.1,2 The Undiagnosed Diseases Network (UDN) brings multiple clinical, research and experimental centers under the same umbrella across the United States to facilitate and scale N-of-1 analyses. Here, we present the first joint analysis of whole genome sequencing data of UDN patients across the network. We introduce new, well-calibrated statistical methods for prioritizing disease genes with de novo recurrence and compound heterozygosity. We also detect pathways enriched with candidate and known diagnostic genes. Our computational analysis, coupled with a systematic clinical review, recapitulated known diagnoses and revealed new disease associations. We further release a software package, RaMeDiES, enabling automated cross-analysis of deidentified sequenced cohorts for new diagnostic and research discoveries. Gene-level findings and variant-level information across the cohort are available in a public-facing browser (https://dbmi-bgm.github.io/udn-browser/). These results show that N-of-1 efforts should be supplemented by a joint genomic analysis across cohorts.
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Affiliation(s)
| | | | | | - Daniel Traviglia
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Xinyun Li
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT
| | | | - Alexander Veit
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Rosario I. Corona
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA
| | - George de V. Carvalho Neto
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA
| | - Julian Willett
- Department of Pathology and Laboratory Medicine, NewYork-Presbyterian Weill Cornell Medical Center, New York, NY
| | - Michele Berselli
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - William Ronchetti
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Stanley F. Nelson
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA
| | - Julian A. Martinez-Agosto
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA
| | - Richard Sherwood
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Joel Krier
- Department of Genetics, Atrius Health, Boston, MA
| | - Isaac S. Kohane
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | | | - Shamil R. Sunyaev
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
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Layo-Carris DE, Lubin EE, Sangree AK, Clark KJ, Durham EL, Gonzalez EM, Smith S, Angireddy R, Wang XM, Weiss E, Toutain A, Mendoza-Londono R, Dupuis L, Damseh N, Velasco D, Valenzuela I, Codina-Solà M, Ziats C, Have J, Clarkson K, Steel D, Kurian M, Barwick K, Carrasco D, Dagli AI, Nowaczyk MJM, Hančárová M, Bendová Š, Prchalova D, Sedláček Z, Baxová A, Nowak CB, Douglas J, Chung WK, Longo N, Platzer K, Klöckner C, Averdunk L, Wieczorek D, Krey I, Zweier C, Reis A, Balci T, Simon M, Kroes HY, Wiesener A, Vasileiou G, Marinakis NM, Veltra D, Sofocleous C, Kosma K, Traeger Synodinos J, Voudris KA, Vuillaume ML, Gueguen P, Derive N, Colin E, Battault C, Au B, Delatycki M, Wallis M, Gallacher L, Majdoub F, Smal N, Weckhuysen S, Schoonjans AS, Kooy RF, Meuwissen M, Cocanougher BT, Taylor K, Pizoli CE, McDonald MT, James P, Roeder ER, Littlejohn R, Borja NA, Thorson W, King K, Stoeva R, Suerink M, Nibbeling E, Baskin S, L E Guyader G, Kaplan J, Muss C, Carere DA, Bhoj EJK, Bryant LM. Expanded phenotypic spectrum of neurodevelopmental and neurodegenerative disorder Bryant-Li-Bhoj syndrome with 38 additional individuals. Eur J Hum Genet 2024; 32:928-937. [PMID: 38678163 PMCID: PMC11291762 DOI: 10.1038/s41431-024-01610-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/27/2024] [Accepted: 04/09/2024] [Indexed: 04/29/2024] Open
Abstract
Bryant-Li-Bhoj syndrome (BLBS), which became OMIM-classified in 2022 (OMIM: 619720, 619721), is caused by germline variants in the two genes that encode histone H3.3 (H3-3A/H3F3A and H3-3B/H3F3B) [1-4]. This syndrome is characterized by developmental delay/intellectual disability, craniofacial anomalies, hyper/hypotonia, and abnormal neuroimaging [1, 5]. BLBS was initially categorized as a progressive neurodegenerative syndrome caused by de novo heterozygous variants in either H3-3A or H3-3B [1-4]. Here, we analyze the data of the 58 previously published individuals along 38 unpublished, unrelated individuals. In this larger cohort of 96 people, we identify causative missense, synonymous, and stop-loss variants. We also expand upon the phenotypic characterization by elaborating on the neurodevelopmental component of BLBS. Notably, phenotypic heterogeneity was present even amongst individuals harboring the same variant. To explore the complex phenotypic variation in this expanded cohort, the relationships between syndromic phenotypes with three variables of interest were interrogated: sex, gene containing the causative variant, and variant location in the H3.3 protein. While specific genotype-phenotype correlations have not been conclusively delineated, the results presented here suggest that the location of the variants within the H3.3 protein and the affected gene (H3-3A or H3-3B) contribute more to the severity of distinct phenotypes than sex. Since these variables do not account for all BLBS phenotypic variability, these findings suggest that additional factors may play a role in modifying the phenotypes of affected individuals. Histones are poised at the interface of genetics and epigenetics, highlighting the potential role for gene-environment interactions and the importance of future research.
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Affiliation(s)
- Dana E Layo-Carris
- Department of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Emily E Lubin
- Department of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Annabel K Sangree
- Department of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kelly J Clark
- Department of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Emily L Durham
- Department of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elizabeth M Gonzalez
- Department of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sarina Smith
- Department of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rajesh Angireddy
- Department of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Xiao Min Wang
- Department of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Erin Weiss
- Department of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Annick Toutain
- Service de Génétique, CHU de Tours, Tours, France
- UMR1253, iBrain, Inserm, University of Tours, Tours, France
| | - Roberto Mendoza-Londono
- Division of Clinical and Metabolic Genetics, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Lucie Dupuis
- Division of Clinical and Metabolic Genetics, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Nadirah Damseh
- Division of Clinical and Metabolic Genetics, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Danita Velasco
- Children's Nebraska, University of Nebraska Medical Center, Omaha, NE, USA
| | - Irene Valenzuela
- Department of Clinical and Molecular Genetics and Rare Disease Unit Hospital Vall d'Hebron, Barcelona, Spain
- Medicine Genetics Group, Vall Hebron Research Institute, Barcelona, Spain
| | - Marta Codina-Solà
- Department of Clinical and Molecular Genetics and Rare Disease Unit Hospital Vall d'Hebron, Barcelona, Spain
- Medicine Genetics Group, Vall Hebron Research Institute, Barcelona, Spain
| | | | - Jaclyn Have
- Shodair Children's Hospital, Helena, MT, USA
| | | | - Dora Steel
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Manju Kurian
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Katy Barwick
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Diana Carrasco
- Department of Clinical Genetics, Cook Children's Hospital, Fort Worth, TX, USA
| | - Aditi I Dagli
- Orlando Health, Arnold Palmer Hospital For Children, Orlando, FL, USA
| | - M J M Nowaczyk
- McMaster University Medical Centre, Hamilton, ON, Canada
| | - Miroslava Hančárová
- Charles University Second Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Šárka Bendová
- Charles University Second Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Darina Prchalova
- Charles University Second Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Zdeněk Sedláček
- Charles University Second Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Alica Baxová
- Charles University First Faculty of Medicine and General University Hospital, Prague, Czech Republic
| | - Catherine Bearce Nowak
- Division of Genetics and Metabolism, Massachusetts General Hospital for Children, Boston, MA, USA
| | | | - Wendy K Chung
- Harvard Medical School, Boston, MA, USA
- Boston Children's Hospital, Boston, MA, USA
| | | | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Chiara Klöckner
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Luisa Averdunk
- Institute of Human Genetics, Heinrich-Heine-University Düsseldorf, Medical Faculty, Düsseldorf, Germany
| | - Dagmar Wieczorek
- Institute of Human Genetics, Heinrich-Heine-University Düsseldorf, Medical Faculty, Düsseldorf, Germany
| | - Ilona Krey
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Christiane Zweier
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
- Department of Human Genetics, Inselspital Bern, University of Bern, Bern, Switzerland
| | - Andre Reis
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Tugce Balci
- University of Western Ontario, London, ON, Canada
| | - Marleen Simon
- Department of Genetics, University Medical Center, Utrecht, Netherlands
| | - Hester Y Kroes
- Department of Genetics, University Medical Center, Utrecht, Netherlands
| | - Antje Wiesener
- Department of Genetics, University Medical Center, Utrecht, Netherlands
| | - Georgia Vasileiou
- Department of Genetics, University Medical Center, Utrecht, Netherlands
| | - Nikolaos M Marinakis
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Danai Veltra
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Christalena Sofocleous
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Konstantina Kosma
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Joanne Traeger Synodinos
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Konstantinos A Voudris
- Second Department of Paediatrics, University of Athens, 'P & A Kyriakou' Children's Hospital, Athens, Greece
| | - Marie-Laure Vuillaume
- Service de Génétique, CHU de Tours, Tours, France
- UMR1253, iBrain, Inserm, University of Tours, Tours, France
- Laboratoire de Biologie Médicale Multi-Sites SeqOIA, Paris, France
| | - Paul Gueguen
- Service de Génétique, CHU de Tours, Tours, France
- UMR1253, iBrain, Inserm, University of Tours, Tours, France
- Laboratoire de Biologie Médicale Multi-Sites SeqOIA, Paris, France
| | - Nicolas Derive
- Laboratoire de Biologie Médicale Multi-Sites SeqOIA, Paris, France
| | - Estelle Colin
- Service de Génétique Médicale, CHU d'Angers, Angers, France
| | | | - Billie Au
- University of Calgary, Calgary, AB, Canada
| | - Martin Delatycki
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Mathew Wallis
- Tasmanian Clinical Genetics Service, Tasmanian Health Service, Hobart, TAS, Australia
- School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Lyndon Gallacher
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Fatma Majdoub
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, Antwerp, Belgium
- Applied and Translational Neurogenomics Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Medical Genetics Department, University Hedi Chaker Hospital of Sfax, Sfax, Tunisia
| | - Noor Smal
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, Antwerp, Belgium
- Applied and Translational Neurogenomics Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Sarah Weckhuysen
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, Antwerp, Belgium
- Applied and Translational Neurogenomics Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Department of Pediatric Neurology, University Hospital Antwerp, Antwerp, Belgium
- Translational Neurosciences, Faculty of Medicine and Health Science, University of Antwerp, Antwerp, Belgium
- NEURO Research Centre of Excellence, University of Antwerp, Antwerp, Belgium
| | - An-Sofie Schoonjans
- Department of Pediatric Neurology, University Hospital Antwerp, Antwerp, Belgium
- Department of Pediatrics, Duke University Hospital, Durham, NC, USA
| | - R Frank Kooy
- Center of Medical Genetics, Antwerp University Hospital/University of Antwerp, Edegem, Belgium
| | - Marije Meuwissen
- Department of Pediatrics, Duke University Hospital, Durham, NC, USA
- Center of Medical Genetics, Antwerp University Hospital/University of Antwerp, Edegem, Belgium
| | | | - Kathryn Taylor
- Division of Pediatric Neurology, Duke University Hospital, Durham, NC, USA
| | - Carolyn E Pizoli
- Division of Pediatric Neurology, Duke University Hospital, Durham, NC, USA
| | - Marie T McDonald
- Division of Medical Genetics, Duke University Hospital, Durham, NC, USA
| | - Philip James
- DMG Children's Rehabilitative Services, Phoenix, AZ, USA
| | - Elizabeth R Roeder
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, USA
| | - Rebecca Littlejohn
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, USA
| | - Nicholas A Borja
- John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Willa Thorson
- John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Kristine King
- Genetics Department, Mary Bridge Children's Hospital, Multicare Health System, Tacoma, WA, USA
| | - Radka Stoeva
- Medical genetics department, Centre Hospitalier, Le Mans, France
| | - Manon Suerink
- Department of Clinical Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Esther Nibbeling
- Department of Clinical Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Stephanie Baskin
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Gwenaël L E Guyader
- Service de Génétique médicale, Centre Labellisé Anomalies du Développement-Ouest Site, Poitiers, France
| | | | | | | | - Elizabeth J K Bhoj
- Department of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Laura M Bryant
- Department of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
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Gippert S, Wagner M, Brunet T, Berruti R, Brugger M, Schwaibold EMC, Haack TB, Hoffmann GF, Bettendorf M, Choukair D. Exome sequencing (ES) of a pediatric cohort with chronic endocrine diseases: a single-center study (within the framework of the TRANSLATE-NAMSE project). Endocrine 2024; 85:444-453. [PMID: 37940764 PMCID: PMC11246252 DOI: 10.1007/s12020-023-03581-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/18/2023] [Indexed: 11/10/2023]
Abstract
BACKGROUND Endocrine disorders are heterogeneous and include a significant number of rare monogenic diseases. METHODS We performed exome sequencing (ES) in 106 children recruited from a single center within the TRANSLATE‑NAMSE project. They were categorized into subgroups: proportionate short stature (PSS), disproportionate short stature (DSS), hypopituitarism (H), differences in sexual development (DSD), syndromic diseases (SD) and others. RESULTS The overall diagnostic yield was 34.9% (n = 37/106), including 5 patients with variants in candidate genes, which have contributed to collaborations to identify gene-disease associations. The diagnostic yield varied significantly between subgroups: PSS: 16.6% (1/6); DSS: 18.8% (3/16); H: 17.1% (6/35); DSD: 37.5% (3/8); SD: 66.6% (22/33); others: 25% (2/8). Confirmed diagnoses included 75% ultrarare diseases. Three patients harbored more than one disease-causing variant, resulting in dual diagnoses. CONCLUSIONS ES is an effective tool for genetic diagnosis in pediatric patients with complex endocrine diseases. An accurate phenotypic description, including comprehensive endocrine diagnostics, as well as the evaluation of variants in multidisciplinary case conferences involving geneticists, are necessary for personalized diagnostic care. Here, we illustrate the broad spectrum of genetic endocrinopathies that have led to the initiation of specific treatment, surveillance, and family counseling.
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Affiliation(s)
- Sebastian Gippert
- Division of Pediatric Endocrinology and Diabetes, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany and Center for Rare Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Matias Wagner
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Institute for Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Theresa Brunet
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Department of Pediatric Neurology and Developmental Medicine, Hauner Children's Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Riccardo Berruti
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Melanie Brugger
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | | | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, Germany and Centre for Rare Diseases, University of Tuebingen, Tübingen, Germany
| | - Georg F Hoffmann
- Division of Pediatric Endocrinology and Diabetes, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany and Center for Rare Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Markus Bettendorf
- Division of Pediatric Endocrinology and Diabetes, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany and Center for Rare Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Daniela Choukair
- Division of Pediatric Endocrinology and Diabetes, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany and Center for Rare Diseases, University Hospital Heidelberg, Heidelberg, Germany.
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Selvam K, Wyrick JJ, Parra MA. DNA Repair in Nucleosomes: Insights from Histone Modifications and Mutants. Int J Mol Sci 2024; 25:4393. [PMID: 38673978 PMCID: PMC11050016 DOI: 10.3390/ijms25084393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 04/08/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
DNA repair pathways play a critical role in genome stability, but in eukaryotic cells, they must operate to repair DNA lesions in the compact and tangled environment of chromatin. Previous studies have shown that the packaging of DNA into nucleosomes, which form the basic building block of chromatin, has a profound impact on DNA repair. In this review, we discuss the principles and mechanisms governing DNA repair in chromatin. We focus on the role of histone post-translational modifications (PTMs) in repair, as well as the molecular mechanisms by which histone mutants affect cellular sensitivity to DNA damage agents and repair activity in chromatin. Importantly, these mechanisms are thought to significantly impact somatic mutation rates in human cancers and potentially contribute to carcinogenesis and other human diseases. For example, a number of the histone mutants studied primarily in yeast have been identified as candidate oncohistone mutations in different cancers. This review highlights these connections and discusses the potential importance of DNA repair in chromatin to human health.
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Affiliation(s)
- Kathiresan Selvam
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - John J. Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - Michael A. Parra
- Department of Chemistry, Susquehanna University, Selinsgrove, PA 17870, USA
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6
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Bell CG. Epigenomic insights into common human disease pathology. Cell Mol Life Sci 2024; 81:178. [PMID: 38602535 PMCID: PMC11008083 DOI: 10.1007/s00018-024-05206-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 04/12/2024]
Abstract
The epigenome-the chemical modifications and chromatin-related packaging of the genome-enables the same genetic template to be activated or repressed in different cellular settings. This multi-layered mechanism facilitates cell-type specific function by setting the local sequence and 3D interactive activity level. Gene transcription is further modulated through the interplay with transcription factors and co-regulators. The human body requires this epigenomic apparatus to be precisely installed throughout development and then adequately maintained during the lifespan. The causal role of the epigenome in human pathology, beyond imprinting disorders and specific tumour suppressor genes, was further brought into the spotlight by large-scale sequencing projects identifying that mutations in epigenomic machinery genes could be critical drivers in both cancer and developmental disorders. Abrogation of this cellular mechanism is providing new molecular insights into pathogenesis. However, deciphering the full breadth and implications of these epigenomic changes remains challenging. Knowledge is accruing regarding disease mechanisms and clinical biomarkers, through pathogenically relevant and surrogate tissue analyses, respectively. Advances include consortia generated cell-type specific reference epigenomes, high-throughput DNA methylome association studies, as well as insights into ageing-related diseases from biological 'clocks' constructed by machine learning algorithms. Also, 3rd-generation sequencing is beginning to disentangle the complexity of genetic and DNA modification haplotypes. Cell-free DNA methylation as a cancer biomarker has clear clinical utility and further potential to assess organ damage across many disorders. Finally, molecular understanding of disease aetiology brings with it the opportunity for exact therapeutic alteration of the epigenome through CRISPR-activation or inhibition.
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Affiliation(s)
- Christopher G Bell
- William Harvey Research Institute, Barts & The London Faculty of Medicine, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK.
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7
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Caballero M, Satterstrom FK, Buxbaum JD, Mahjani B. Identification of moderate effect size genes in autism spectrum disorder through a novel gene pairing approach. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.03.24305278. [PMID: 38633780 PMCID: PMC11023658 DOI: 10.1101/2024.04.03.24305278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Autism Spectrum Disorder (ASD) arises from complex genetic and environmental factors, with inherited genetic variation playing a substantial role. This study introduces a novel approach to uncover moderate effect size (MES) genes in ASD, which individually do not meet the ASD liability threshold but collectively contribute when paired with specific other MES genes. Analyzing 10,795 families from the SPARK dataset, we identified 97 MES genes forming 50 significant gene pairs, demonstrating a substantial association with ASD when considered in tandem, but not individually. Our method leverages familial inheritance patterns and statistical analyses, refined by comparisons against control cohorts, to elucidate these gene pairs' contribution to ASD liability. Furthermore, expression profile analyses of these genes in brain tissues underscore their relevance to ASD pathology. This study underscores the complexity of ASD's genetic landscape, suggesting that gene combinations, beyond high impact single-gene mutations, significantly contribute to the disorder's etiology and heterogeneity. Our findings pave the way for new avenues in understanding ASD's genetic underpinnings and developing targeted therapeutic strategies.
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Affiliation(s)
- Madison Caballero
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - F Kyle Satterstrom
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Joseph D. Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Behrang Mahjani
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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8
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Harris JR, Gao CW, Britton JF, Applegate CD, Bjornsson HT, Fahrner JA. Five years of experience in the Epigenetics and Chromatin Clinic: what have we learned and where do we go from here? Hum Genet 2024; 143:607-624. [PMID: 36952035 PMCID: PMC10034257 DOI: 10.1007/s00439-023-02537-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 02/20/2023] [Indexed: 03/24/2023]
Abstract
The multidisciplinary Epigenetics and Chromatin Clinic at Johns Hopkins provides comprehensive medical care for individuals with rare disorders that involve disrupted epigenetics. Initially centered on classical imprinting disorders, the focus shifted to the rapidly emerging group of genetic disorders resulting from pathogenic germline variants in epigenetic machinery genes. These are collectively called the Mendelian disorders of the epigenetic machinery (MDEMs), or more broadly, Chromatinopathies. In five years, 741 clinic visits have been completed for 432 individual patients, with 153 having confirmed epigenetic diagnoses. Of these, 115 individuals have one of 26 MDEMs with every single one exhibiting global developmental delay and/or intellectual disability. This supports prior observations that intellectual disability is the most common phenotypic feature of MDEMs. Additional common phenotypes in our clinic include growth abnormalities and neurodevelopmental issues, particularly hypotonia, attention-deficit/hyperactivity disorder (ADHD), and anxiety, with seizures and autism being less common. Overall, our patient population is representative of the broader group of MDEMs and includes mostly autosomal dominant disorders impacting writers more so than erasers, readers, and remodelers of chromatin marks. There is an increased representation of dual function components with a reader and an enzymatic domain. As expected, diagnoses were made mostly by sequencing but were aided in some cases by DNA methylation profiling. Our clinic has helped to facilitate the discovery of two new disorders, and our providers are actively developing and implementing novel therapeutic strategies for MDEMs. These data and our high follow-up rate of over 60% suggest that we are achieving our mission to diagnose, learn from, and provide optimal care for our patients with disrupted epigenetics.
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Affiliation(s)
- Jacqueline R Harris
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Kennedy Krieger Institute, Baltimore, MD, USA
| | - Christine W Gao
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Johns Hopkins Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jacquelyn F Britton
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Carolyn D Applegate
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hans T Bjornsson
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Landspitali University Hospital, Reykjavik, Iceland
| | - Jill A Fahrner
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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9
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Yamamoto S, Kanca O, Wangler MF, Bellen HJ. Integrating non-mammalian model organisms in the diagnosis of rare genetic diseases in humans. Nat Rev Genet 2024; 25:46-60. [PMID: 37491400 DOI: 10.1038/s41576-023-00633-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2023] [Indexed: 07/27/2023]
Abstract
Next-generation sequencing technology has rapidly accelerated the discovery of genetic variants of interest in individuals with rare diseases. However, showing that these variants are causative of the disease in question is complex and may require functional studies. Use of non-mammalian model organisms - mainly fruitflies (Drosophila melanogaster), nematode worms (Caenorhabditis elegans) and zebrafish (Danio rerio) - enables the rapid and cost-effective assessment of the effects of gene variants, which can then be validated in mammalian model organisms such as mice and in human cells. By probing mechanisms of gene action and identifying interacting genes and proteins in vivo, recent studies in these non-mammalian model organisms have facilitated the diagnosis of numerous genetic diseases and have enabled the screening and identification of therapeutic options for patients. Studies in non-mammalian model organisms have also shown that the biological processes underlying rare diseases can provide insight into more common mechanisms of disease and the biological functions of genes. Here, we discuss the opportunities afforded by non-mammalian model organisms, focusing on flies, worms and fish, and provide examples of their use in the diagnosis of rare genetic diseases.
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Affiliation(s)
- Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.
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10
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Agata A, Ohtsuka S, Noji R, Gotoh H, Ono K, Nomura T. A Neanderthal/Denisovan GLI3 variant contributes to anatomical variations in mice. Front Cell Dev Biol 2023; 11:1247361. [PMID: 38020913 PMCID: PMC10651735 DOI: 10.3389/fcell.2023.1247361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 10/12/2023] [Indexed: 12/01/2023] Open
Abstract
Changes in genomic structures underlie phenotypic diversification in organisms. Amino acid-changing mutations affect pleiotropic functions of proteins, although little is known about how mutated proteins are adapted in existing developmental programs. Here we investigate the biological effects of a variant of the GLI3 transcription factor (GLI3R1537C) carried in Neanderthals and Denisovans, which are extinct hominins close to modern humans. R1537C does not compromise protein stability or GLI3 activator-dependent transcriptional activities. In contrast, R1537C affects the regulation of downstream target genes associated with developmental processes. Furthermore, genome-edited mice carrying the Neanderthal/Denisovan GLI3 mutation exhibited various alterations in skeletal morphology. Our data suggest that an extinct hominin-type GLI3 contributes to species-specific anatomical variations, which were tolerated by relaxed constraint in developmental programs during human evolution.
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Affiliation(s)
- Ako Agata
- Developmental Neurobiology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Satoshi Ohtsuka
- Laboratories for Experimental Animals, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Ryota Noji
- Developmental Neurobiology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hitoshi Gotoh
- Developmental Neurobiology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Katsuhiko Ono
- Developmental Neurobiology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tadashi Nomura
- Developmental Neurobiology, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Applied Biology, Kyoto Institute of Technology, Kyoto, Japan
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11
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Feng L, Barrows D, Zhong L, Mätlik K, Porter EG, Djomo AM, Yau I, Soshnev AA, Carroll TS, Wen D, Hatten ME, Garcia BA, Allis CD. Altered chromatin occupancy of patient-associated H4 mutants misregulate neuronal differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.29.560141. [PMID: 37808786 PMCID: PMC10557780 DOI: 10.1101/2023.09.29.560141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Chromatin is a crucial regulator of gene expression and tightly controls development across species. Mutations in only one copy of multiple histone genes were identified in children with developmental disorders characterized by microcephaly, but their mechanistic roles in development remain unclear. Here we focus on dominant mutations affecting histone H4 lysine 91. These H4K91 mutants form aberrant nuclear puncta at specific heterochromatin regions. Mechanistically, H4K91 mutants demonstrate enhanced binding to the histone variant H3.3, and ablation of H3.3 or the H3.3-specific chaperone DAXX diminishes the mutant localization to chromatin. Our functional studies demonstrate that H4K91 mutant expression increases chromatin accessibility, alters developmental gene expression through accelerating pro-neural differentiation, and causes reduced mouse brain size in vivo, reminiscent of the microcephaly phenotypes of patients. Together, our studies unveil a distinct molecular pathogenic mechanism from other known histone mutants, where H4K91 mutants misregulate cell fate during development through abnormal genomic localization.
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Affiliation(s)
- Lijuan Feng
- The Rockefeller University, Laboratory of Chromatin Biology and Epigenetics, New York, NY
| | - Douglas Barrows
- The Rockefeller University, Bioinformatics Resource Center, New York, NY
| | - Liangwen Zhong
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY
| | - Kärt Mätlik
- The Rockefeller University, Laboratory of Developmental Neurobiology, New York, NY
| | - Elizabeth G. Porter
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
| | - Annaelle M. Djomo
- The Rockefeller University, Laboratory of Chromatin Biology and Epigenetics, New York, NY
| | - Iris Yau
- The Rockefeller University, Laboratory of Chromatin Biology and Epigenetics, New York, NY
- Hunter College of the City University of New York, Yalow Honors Scholar Program, New York, NY
| | - Alexey A. Soshnev
- The Rockefeller University, Laboratory of Chromatin Biology and Epigenetics, New York, NY
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San Antonio, San Antonio, TX
| | - Thomas S. Carroll
- The Rockefeller University, Bioinformatics Resource Center, New York, NY
| | - Duancheng Wen
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY
| | - Mary E. Hatten
- The Rockefeller University, Laboratory of Developmental Neurobiology, New York, NY
| | - Benjamin A. Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
| | - C. David Allis
- The Rockefeller University, Laboratory of Chromatin Biology and Epigenetics, New York, NY
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12
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Cheng J, Novati G, Pan J, Bycroft C, Žemgulytė A, Applebaum T, Pritzel A, Wong LH, Zielinski M, Sargeant T, Schneider RG, Senior AW, Jumper J, Hassabis D, Kohli P, Avsec Ž. Accurate proteome-wide missense variant effect prediction with AlphaMissense. Science 2023; 381:eadg7492. [PMID: 37733863 DOI: 10.1126/science.adg7492] [Citation(s) in RCA: 317] [Impact Index Per Article: 317.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 08/23/2023] [Indexed: 09/23/2023]
Abstract
The vast majority of missense variants observed in the human genome are of unknown clinical significance. We present AlphaMissense, an adaptation of AlphaFold fine-tuned on human and primate variant population frequency databases to predict missense variant pathogenicity. By combining structural context and evolutionary conservation, our model achieves state-of-the-art results across a wide range of genetic and experimental benchmarks, all without explicitly training on such data. The average pathogenicity score of genes is also predictive for their cell essentiality, capable of identifying short essential genes that existing statistical approaches are underpowered to detect. As a resource to the community, we provide a database of predictions for all possible human single amino acid substitutions and classify 89% of missense variants as either likely benign or likely pathogenic.
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13
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Liu CP, Yu Z, Xiong J, Hu J, Song A, Ding D, Yu C, Yang N, Wang M, Yu J, Hou P, Zeng K, Li Z, Zhang Z, Zhang X, Li W, Zhang Z, Zhu B, Li G, Xu RM. Structural insights into histone binding and nucleosome assembly by chromatin assembly factor-1. Science 2023; 381:eadd8673. [PMID: 37616371 PMCID: PMC11186048 DOI: 10.1126/science.add8673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 07/19/2023] [Indexed: 08/26/2023]
Abstract
Chromatin inheritance entails de novo nucleosome assembly after DNA replication by chromatin assembly factor-1 (CAF-1). Yet direct knowledge about CAF-1's histone binding mode and nucleosome assembly process is lacking. In this work, we report the crystal structure of human CAF-1 in the absence of histones and the cryo-electron microscopy structure of CAF-1 in complex with histones H3 and H4. One histone H3-H4 heterodimer is bound by one CAF-1 complex mainly through the p60 subunit and the acidic domain of the p150 subunit. We also observed a dimeric CAF-1-H3-H4 supercomplex in which two H3-H4 heterodimers are poised for tetramer assembly and discovered that CAF-1 facilitates right-handed DNA wrapping of H3-H4 tetramers. These findings signify the involvement of DNA in H3-H4 tetramer formation and suggest a right-handed nucleosome precursor in chromatin replication.
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Affiliation(s)
- Chao-Pei Liu
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhenyu Yu
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jun Xiong
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jie Hu
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Aoqun Song
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Dongbo Ding
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Cong Yu
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences; Hangzhou, Zhejiang 310024, China
| | - Na Yang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of Tianjin, Nankai University, Tianjin 300353, China
| | - Mingzhu Wang
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
| | - Juan Yu
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Peini Hou
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Kangning Zeng
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenyu Li
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuqiang Zhang
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xinzheng Zhang
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Li
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Department of Pediatrics and Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Bing Zhu
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Guohong Li
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui-Ming Xu
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences; Hangzhou, Zhejiang 310024, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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14
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Borja N, Borjas-Mendoza P, Bivona S, Peart L, Gonzalez J, Johnson BK, Guo S, Yusupov R, Bademci G, Tekin M. H4C5 missense variant leads to a neurodevelopmental phenotype overlapping with Angelman syndrome. Am J Med Genet A 2023; 191:1911-1916. [PMID: 36987712 PMCID: PMC10286100 DOI: 10.1002/ajmg.a.63193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/29/2023] [Accepted: 03/18/2023] [Indexed: 03/30/2023]
Abstract
Recurrent de novo missense variants in H4 histone genes have recently been associated with a novel neurodevelopmental syndrome that is characterized by intellectual disability and developmental delay as well as more variable findings that include short stature, microcephaly, and facial dysmorphisms. A 4-year-old male with autism, developmental delay, microcephaly, and a happy demeanor underwent evaluation through the Undiagnosed Disease Network. He was clinically suspected to have Angelman syndrome; however, molecular testing was negative. Genome sequencing identified the H4 histone gene variant H4C5 NM_003545.4: c.295T>C, p.Tyr99His, which parental testing confirmed to be de novo. The variant met criteria for a likely pathogenic classification and is one of the seven known disease-causing missense variants in H4C5. A comparison of our proband's findings to the initial description of the H4-associated neurodevelopmental syndrome demonstrates that his phenotype closely matches the spectrum of those reported among the 29 affected individuals. As such, this report corroborates the delineation of neurodevelopmental syndrome caused by de novo missense H4 gene variants. Moreover, it suggests that cases of clinically suspected Angelman syndrome without molecular confirmation should undergo exome or genome sequencing, as novel neurodevelopmental syndromes with phenotypes overlapping with Angelman continue to be discovered.
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Affiliation(s)
- Nicholas Borja
- John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Paulo Borjas-Mendoza
- John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Stephanie Bivona
- John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - LéShon Peart
- John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Joanna Gonzalez
- John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Brittney Keira Johnson
- John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Shengru Guo
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Roman Yusupov
- Department of Clinical Genetics, Memorial Healthcare System, Hollywood, Florida, USA
| | | | - Guney Bademci
- John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Mustafa Tekin
- John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
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15
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Whiwon L, Salma S, Daniel A, Stephanie L, Marc C, Cherith S, Abby T, Angela S, Robin H, Yvonne B. Patient-facing digital tools for delivering genetic services: a systematic review. J Med Genet 2023; 60:1-10. [PMID: 36137613 DOI: 10.1136/jmg-2022-109085] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/19/2022] [Indexed: 01/24/2023]
Abstract
This study systematically reviewed the literature on the impact of digital genetics tools on patient care and system efficiencies. MEDLINE and Embase were searched for articles published between January 2010 and March 2021. Studies evaluating the use of patient-facing digital tools in the context of genetic service delivery were included. Two reviewers screened and extracted patient-reported and system-focused outcomes from each study. Data were synthesised using a descriptive approach. Of 3226 unique studies identified, 87 were included. A total of 70 unique digital tools were identified. As a result of using digital tools, 84% of studies reported a positive outcome in at least one of the following patient outcomes: knowledge, psychosocial well-being, behavioural/management changes, family communication, decision-making or level of engagement. Digital tools improved workflow and efficiency for providers and reduced the amount of time they needed to spend with patients. However, we identified a misalignment between study purpose and patient-reported outcomes measured and a lack of tools that encompass the entire genetic counselling and testing trajectory. Given increased demand for genetic services and the shift towards virtual care, this review provides evidence that digital tools can be used to efficiently deliver patient-centred care. Future research should prioritise development, evaluation and implementation of digital tools that can support the entire patient trajectory across a range of clinical settings. PROSPERO registration numberCRD42020202862.
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Affiliation(s)
- Lee Whiwon
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Shickh Salma
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Assamad Daniel
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Luca Stephanie
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Clausen Marc
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Somerville Cherith
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Tafler Abby
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Shaw Angela
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Hayeems Robin
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Bombard Yvonne
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
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